Actually never mind, the following seems to work:
def delete_chain():
def first_residue(mol_id,ch_id):
result=seqnum_from_serial_number(mol_id,"%s"%(ch_id),0)
return result
def last_residue(mol_id,ch_id):
n=chain_n_residues(ch_id,mol_id)-1
result=seqnum_from_serial_number(mol_id,"%s"%(ch_id),n)
return result
active_mol_id=active_residue()[0]
active_chain_id=active_residue()[1]
first_res=first_residue(active_mol_id,active_chain_id)
last_res=last_residue(active_mol_id,active_chain_id)
delete_residue_range(active_mol_id,active_chain_id,first_res,last_res)
menu=coot_menubar_menu("Custom")
add_simple_coot_menu_menuitem(menu,"Delete active chain", lambda func: delete_chain())
On Mar 12, 2014, at 9:52 AM, Oliver Clarke <[log in to unmask]> wrote:
> Thanks Bernhard, that’s very helpful.
>
> Using that function, I wrote a little script that will delete a chain based on the currently selected residue:
>
> def first_residue(mol_id,ch_id):
> result=seqnum_from_serial_number(mol_id,"%s"%(ch_id),0)
> return result
> def last_residue(mol_id,ch_id):
> n=chain_n_residues(ch_id,mol_id)-1
> result=seqnum_from_serial_number(mol_id,"%s"%(ch_id),n)
> return result
> active_mol_id=active_residue()[0]
> active_chain_id=active_residue()[1]
> first_res=first_residue(active_mol_id,active_chain_id)
> last_res=last_residue(active_mol_id,active_chain_id)
> delete_residue_range(active_mol_id,active_chain_id,first_res,last_res)
>
>
> I’d quite like to assign this to a button, but the user defined button interface in coot only seems to take one-line commands, not multi-line - I guess I can assign it to a key binding though. Or is there an easy way to add a user-defined menu item?
>
> Oliver.
> On Mar 12, 2014, at 3:08 AM, Bernhard Lohkamp <[log in to unmask]> wrote:
>
>>
>> Hi Oliver,
>>
>> You can use the scripting function delete_residue_range (https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#index-delete_002dresidue_002drange-709):
>>
>> delete_residue_range(imol, chain_id, start_res, stop_res)
>>
>> Maybe not exactly what you want, but that works fine for this purpose (*). You can give a residue range outside what you have, just to make sure everything is deleted, i.e. delete_residue_range(0,"A", -100,100000).
>>
>> B
>>
>> (*) Incidentally it has been on my todo list for quite some time to make a delete chain (etc) function...
>>
>> On 12/03/2014 00:51, Oliver Clarke wrote:
>>> Another one to chalk on the list of things that would be nice to have but not really needed - I feel like having a delete chain option in the ‘Delete item’ dialog would be very handy…
>>>
>>> I often find myself needing to delete a chain (from a complex or oligomer for example), and I always switch the color to Jone’s Rainbow and then hunt around for the N- and C- termini and use delete zone, which works but is a little cumbersome.
>>>
>>> Being able to click on a single atom from the desired chain to delete it would speed things up tremendously, for example when editing the kind of spaghetti-model that sometimes comes out of buccaneer or Arp/warp at low resolution (where there a lot of peptide fragments that need cleaning up).
>>>
>>> Best,
>>> Oliver.
>>>
>>
>> --
>> ***************************************************
>>
>> Dr. Bernhard Lohkamp
>> Associate Professor/Docent
>> Div. Molecular Structural Biology
>> Dept. of Medical Biochemistry and Biophysics (MBB)
>> Karolinska Institutet
>> S-17177 Stockholm
>> Sweden
>>
>> phone: (+46) 08-52487651
>> fax: (+46) 08-327626
>> email: [log in to unmask]
>
